Grease Pencil strokes from movie clip editor not showing in 3D view
I figured out a workaround! So what I ended up doing was to write a small script to change all the 2D strokes I made to 3D strokes:

gp = bpy.context.scene.grease_pencil
for l in gp.layers:
    for f in l.frames:
        for s in f.strokes:
            s.draw_mode='3DSPACE'


For some reason which I do not know, the 3D strokes were the correct orientation when I viewed them from the top orthographic view. Then I scaled and moved my background image to be behind the strokes the same way I had it before.